Hi Drew,
are you sure that you are installing 64bit version? This
https://anaconda.org/rdkit/rdkit says that the version you have installed is
present in win-32 build if I am not mistaken.
Best,
Lukas
From: Drew Gibson via Rdkit-discuss
Reply-To: Drew Gibson
Date: Saturday, 9 June
Dear all,
I’ve just recently started using rdkit in python. Btw. A very nice piece of
work. First, I’d like to generate 2D depiction of molecules I’m constructing
from 3D coordinate data. I’m aware of methods such as
GenerateDepictionMatching2DStructure(…) and
Dear rdkiters,
I’m constructing molecules from scratch using python 3.5.4 and RDKit 2017.09.2
and due to the variety of reasons some of them are violating general principles
of chemistry in a way implemented in rdkit, so I’m getting information like:
Explicit valence for atom # 14 N, 4,
here:
https://www.ebi.ac.uk/pdbe/about/jobs
Cheers,
Lukas Pravda, Ph.D.
Bioinformatician/Scientific Programmer
Protein Data Bank in Europe (PDBe)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
United Kingdom
: Greg Landrum <greg.land...@gmail.com>
Date: Thursday, 22 February 2018 at 13:32
To: Lukas Pravda <lpra...@ebi.ac.uk>
Cc: RDKit Discuss <Rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Programatic access to the mol sanitation process
results
Hi Lukas,
On
)
error_msg = out_stream.getvalue().decode('utf-8')
print(error_msg)
Lukas
From: Peter Gedeck <peter.ged...@gmail.com>
Date: Friday, 9 March 2018 at 15:02
To: Lukas Pravda <lpra...@ebi.ac.uk>
Cc: Greg Landrum <greg.land...@gmail.com>, <Rdkit-discuss@lists.sourceforge.net
Hi all,
First of all, my configuration is following:
macOS: 10.14
conda: 4.5.11
python: 3.6.6
rdkit: 2018.09.01
I just tried to set bond width for 2D SVG images and I run into situation I
don’t understand much (nothing surprising ☺). I’m aware of 2 ways how to
generate SVG images
Hi all,
I’m playing with the Coordgen library inside rdkit and I have a couple of
questions I could not figure out by myself. Hopefully someone more experienced
will know.
[comment] The way one can pass a scaling factor to the bond size is very
unintuitive. If I don’t provide any
Hi Jean-Marc,
Just a thought, but SDMolSupplier has a lazy eval, if I am not mistaken.
Technically you should get all the rdkit warnings and errors at the time of
processing that bit of the sdf file. You can always read the stderror output,
parse it and throw exception every time a 'funny'
: Greg Landrum
Date: Tuesday, 4 December 2018 at 17:24
To: Lukas Pravda
Cc: RDKIT mailing list
Subject: Re: [Rdkit-discuss] Bond tags in SVGs
Hi Lukas,
There's not currently a way to do this at the moment. The closest you can get
is by calling AddMoleculeMetadata():
In [6]: d
Hi all,
I was wondering if there is a way how you can tag elements (bonds) in
the svg created by rdkit.
i.e. transform something like this:
Into:
Or similar. I’ve found possibility of tagging atoms in the SVG using
Draw.rdMolDraw2D.MolDraw2DSVG.drawOptions() method that
, including structural and functional
annotations, domains, ligand-binding sites and interfaces. In the next step we
would like to present a similar aggregated view from a small molecule / ligand
perspective.
Thank you for your time,
Lukas
--
Lukas Pravda, Ph.D.
Bioinformatician/Scientific
Hi Illimar,
If you need to access coordinates without creating conformer object do you
really need to use rdkit I the first place? PDB file is column based format, so
extracting coordinates for atoms for example with python is very
straightforward.
Lukas
--
Lukas
Hi Greg,
I was wondering If you managed to create the Mac build you were talking about
some time ago. Also I wonder If this functionality is going to be part of the
next RDKit release?
Best,
Lukas
From: Greg Landrum
Date: Tuesday, 5 February 2019 at 14:45
To: Lukas Pravda
Cc
at 17:49
To: Lukas Pravda
Cc: RDKIT mailing list
Subject: Re: [Rdkit-discuss] Bond tags in SVGs
Hi Lukas,
I had a chance to do a bit of work on this recently and I'd be interested to
hear your feedback.
Bonds are now tagged with their bond IDs (using classes) and the "Tag
If it is not too much trouble to ask, please build it for mac os (10.14.3)
python 3.6.x.
Thanks!
Lukas
From: Greg Landrum
Date: Tuesday, 5 February 2019 at 13:40
To: Lukas Pravda
Cc: RDKIT mailing list
Subject: Re: [Rdkit-discuss] Bond tags in SVGs
On Tue, Feb 5, 2019 at 12
Hi Pat,
>From my experience rdkit uses more or less 1.5 units bond length for 2D
>depictions. So it makes sense if you rescale your template so that the bond
>length is 1.5.
This is the code snippet I use for the same thing to upscale template with bond
lengths 1.0 to 1.5
import
Dear all,
I construct my own rdkit.Mol objects from mmcif files. I wanted to use
mol.GetNumAtoms(onlyExplicit=True) to get the number of heavy atoms for that
molecule, however, I have noticed that the function returns all the time number
of all atoms in the molecule including hydrogens (47
(now explicitOnly) returns heavy atoms.
Thanks
Lukas
From: Paolo Tosco
Date: Wednesday, 1 May 2019 at 15:32
To: Lukas Pravda , RDKIT mailing list
Subject: Re: [Rdkit-discuss] Get num of heavy atoms returns incorrect value
mol.GetNumHeavyAtoms
Evangelidis
Date: Tuesday, 9 April 2019 at 15:43
To: Lukas Pravda
Cc: Jose Manuel Gally , RDKIT mailing list
Subject: Re: [Rdkit-discuss] Which method to prefer for computing 2D coordinates
Hello Lukas,
I am also struggling with 2D coordinate generation quite a long time as well as
what
Hi Jose,
As you have shown there is no single method which would be perfect for
everything. If you don’t care that much about speed, the possible solution
could be to compute coordinates with all three approaches and then simply
select the best conformer based on some criteria.
The solution I
')
Chem.WrapLogs()
mol = Chem.MolFromSmiles('c1c1(C)(C)')
log.close()
sys.stderr = saved_std_err
works
Lukas
From: Brian Lee
Date: Wednesday, 25 September 2019 at 20:55
To:
Cc: RDKIT mailing list , Lukas Pravda
Subject: Re: [Rdkit-discuss] Fwd: sending warnings to stderr
atom tags (which randomly fixed
those couple of issues, but apparently broke everything else down.
I was wondering how does rdkit work out R/S from inchi string?
Lukas
From: Greg Landrum
Date: Wednesday, 30 October 2019 at 04:28
To: Lukas Pravda
Cc: RDKIT mailing list
Subject: Re
Hi IIllimar,
I don’t really know what your use case is, so it may be completely useless.
However, just to add my two cents, we've created a package that builds on the
top of rdkit and parses PDB ligand definitions from cif files. You can find the
package here:
Hi Mike,
The following code works for me:
import sys
from io import StringIO
from rdkit import Chem
saved_std_err = sys.stderr
log = sys.stderr = StringIO()
Chem.WrapLogs()
# do whatever you want with rdkit
whatever_used_to_be_printed_by_rdkit_in_console_as_str =
Hi Sebastian,
Quickly looking at the available builds in the rdkit conda channel
(https://anaconda.org/rdkit/rdkit) it appears that you are pulling windows
32-bit version of rdkit. Perhaps this is caused by the fact that you use 32bit
version of conda? Try installing 64-bit version of conda
Dear rdkit community,
I’m not quite sure if this is more of an rdkit or a chemistry related question.
I’d like to understand why a manganese ion has 3 radical electrons when
interpreted by rdkit. I have not seen radicals in any other metal ion so far.
The code to get the depiction looks
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